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CPP source MRI

This is a set of functions to prepare a source fMRI dataset for BIDSification and analyses

This can perform:

  • 3D to 4D nii files conversion

  • anatomical defacing [ W I P ]

  • gzip the nii files in a BIDS raw folder

The core functions are in the src folder. This set of functions is intended to be added manually as a submodule to the analysis repo forked from template_fMRI_analysis

How to install and use this template

Add as a submodule

  1. Open the terminal and navigate to your analysis folder forked from template_fMRI_analysis and cloned locally

  2. Type

# navigate to the `lib` folder
cd lib

# add the submodule
git submodule add https://github.com/cpp-lln-lab/CPP_sourceMRI

# initialize the nested submodule(s)
git submodule update --init --recursive
  1. commit the new changes (the new submodule(s))

Dependencies

Make sure that the following toolboxes are installed path.

For instructions see the following links:

Dependencies Used version
Matlab 20???
or octave 4.?
SPM12 v7487
CPP_SPM* > 0.1.0

*already "installed" in template_fMRI_analysis and cloned locally

Contributing

Feel free to open issues to report a bug and ask for improvements.

If you want to contribute, have a look at our contributing guidelines that are meant to guide you and help you get started. If something is not clear or you get stuck: it is more likely we did not do good enough a job at explaining things. So do not hesitate to open an issue, just to ask for clarification.